Thanks. I found the section 6. When I read it. I just get very confused. There seems to be knowledge there that I don't know about. Easier way for me to read it?
That's ok

. Let me see if I can clarify it for you a bit. An OTA update will include the following:
1) A new boot image - this includes things like the new included kernel, and anything else required by the system to boot up.
2) A new system image - this is the actual ROM, as in Android System itself. When you see that your software version is 3.70.651.1, that means your ROM, which exists in the /system image, is based on that version.
3) An hboot image - this is basically your bootloader. When this gets updated, you will lose root if your root method was via the eng bootloader. If your root method was unrevoked, you'll keep S-OFF, but previous nandroid backups will no longer work. If there is no root exploit for a particular new hboot yet, if anything goes wrong, you could get in trouble.
4) A recovery image - You need a custom recovery to take advantage of full root. You can't accept an OTA update while rooted, anyway, as this is used as a part of the update, to begin with. In any case, this is the stock recovery, and is useless to you while you have root.
5) The stock splash screen - this is the initial white screen you see when you turn the phone on.
6) A new radio image - this is a new firmware version for your radio. For best results, you should run the latest radio version, ROM version, and kernel version together. Any other combination could be either unbootable or unstable. For example, updating the radio version, but not updating the ROM or kernel will result in not being able to boot. You *could* use a custom kernel to boot, but you might still have instability.
7) PRI and NV images - PRI, especially, has the same warnings as the radio. Don't use a newer PRI, and an older ROM/kernel. Sometimes you need to use an older PRI with a newer ROM, though, if you have battery life issues.
8) Wimax radio image - this updates your wimax radio version.
We also have these things called RUUs. An RUU is a ROM Update Utility, and it contains basically the same thing as a normal OTA update. The only difference is that an RUU will include an almost empty data image. What that means is that if you update via an OTA update, you'll get all the above images, but your apps, data, and settings stay in tact. If you update with an RUU (or a PC36IMG.zip file that includes the contents of an RUU), you get the same thing, but it wipes out your apps, data, and settings. (To those reading this who might care, you can pull whatever images you want out of a PC36IMG.zip file, so if you wanted to keep data while flashing a PC36IMG.zip RUU, just pull out userdata.img, for example).
All of this is to say that if you update via an OTA update or an RUU, you update too much while you have root. You don't want to do that. All you need while rooted are the new radio images (radio, wimax, pri, nv) and a system image. Now, as you have root, if you updated with a system image from an RUU (OTA update, basically), you would lose root in your ROM. That's not a huge deal, as you can flash whatever you want with S-OFF, but there's little point in wasting your time with that. So, you need to flash the radios (as a package or separately), then flash a rooted ROM based on the new OTA, whether it be a custom ROM or stock one that has been rooted.
If you read those instructions in section 6, you will find links for both of those things. In doing so, you will note that you will not be updating recovery, hboot, the splash screen (always the same with stock), or an entire boot image. You need to keep your custom recovery, and as stated before, updating hboot is bad (unroots if rooted via eng bootloader, and makes nandroid backup useless no matter what rooting method you used). As for the boot image, a custom ROM will include the boot image it needs.
If you are just on stock, there is another option. There is a link in the instructions to flash something called Sprint Lovers ROM, via PC36IMG.zip. That is basically everything you need, as it is basically a RUU, minus the recovery and hboot updates, and a rooted stock ROM in place of the unrooted stock one. It will include all necessary radio updates. If you go that route, it's assumed you want to stick with a close to stock ROM. Otherwise, it's faster to update the radios manually, then flash whatever ROM you like.
I'm sure you still have questions about this, so feel free to ask if anything is still not clear.